HEADER HYDROLASE 18-FEB-13 3ZNV TITLE CRYSTAL STRUCTURE OF THE OTU DOMAIN OF OTULIN AT 1.3 ANGSTROMS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FAM105B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: OTU DOMAIN, RESIDUES 80-352; COMPND 5 EC: 3.4.19.12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA PLACI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: POPINF KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KEUSEKOTTEN,P.R.ELLIOTT,L.GLOCKNER,Y.KULATHU,T.WAUER,D.KRAPPMANN, AUTHOR 2 K.HOFMANN,D.KOMANDER REVDAT 1 26-JUN-13 3ZNV 0 JRNL AUTH K.KEUSEKOTTEN,P.R.ELLIOTT,L.GLOCKNER,B.K.FIIL,R.B.DAMGAARD, JRNL AUTH 2 Y.KULATHU,T.WAUER,M.K.HOSPENTHAL,M.GYRD-HANSEN,D.KRAPPMANN, JRNL AUTH 3 K.HOFMANN,D.KOMANDER JRNL TITL OTULIN ANTAGONIZES LUBAC SIGNALING BY SPECIFICALLY JRNL TITL 2 HYDROLYZING MET1-LINKED POLYUBIQUITIN. JRNL REF CELL(CAMBRIDGE,MASS.) V. 153 1312 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 23746843 JRNL DOI 10.1016/J.CELL.2013.05.014 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.68 REMARK 3 NUMBER OF REFLECTIONS : 69951 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.12680 REMARK 3 R VALUE (WORKING SET) : 0.12532 REMARK 3 FREE R VALUE : 0.15439 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 3720 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.300 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.334 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5140 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.161 REMARK 3 BIN FREE R VALUE SET COUNT : 257 REMARK 3 BIN FREE R VALUE : 0.202 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2343 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 333 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.750 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49 REMARK 3 B22 (A**2) : -0.63 REMARK 3 B33 (A**2) : 0.14 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.040 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.053 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2443 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2357 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3346 ; 1.663 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5463 ; 0.887 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 324 ; 5.676 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;33.648 ;24.463 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 452 ;13.352 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;18.639 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 370 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2793 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 566 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 53 ; 0.294 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 5 ; 0.367 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.078 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 80 ; 0.33 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.283 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.144 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1144 ; 3.842 ; 1.349 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1143 ; 3.834 ;307.79 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1443 ; 4.055 ; 2.024 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1299 ; 4.455 ; 1.653 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1875 ; 4.834 ; 2.346 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2438 ; 9.723 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2363 ;17.856 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 3 REFINED INDIVIDUALLY SIDE CHAINS ARE NOT OBSERVED FOR REMARK 3 RESIDUES 176,178,180,182,206,252,325,346. REMARK 3 DISORDERED SIDE CHAINS WERE PRUNED ACCORDING TO REMARK 3 INTERPRETATION OF THE ELECTRON DENSITY. WATER MOLECULE A 2079 REMARK 3 OCCUPIES THE SAME POSITION AS HIS 339 NEZ ALT B. IN REFINEMENT REMARK 3 THE OCCUPANCY OF THIS WATER WAS IN THE SAME GROUP AS HIS 339 ALT REMARK 3 A AND THUS THEIR OCCUPANCIES WERE REFINED TO ALLOW THE WATER REMARK 3 TO OCCUPY THIS POSITION WHEN HIS ALT A IS OCCUPIED AND NOT TO REMARK 3 OCCUPY THIS POSITION WHEN HIS ALT B IS OCCUPIED. REMARK 4 REMARK 4 3ZNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-13. REMARK 100 THE PDBE ID CODE IS EBI-55864. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315R) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73748 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.30 REMARK 200 RESOLUTION RANGE LOW (A) : 29.26 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.9 REMARK 200 R MERGE (I) : 0.11 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.30 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.9 REMARK 200 R MERGE FOR SHELL (I) : 0.33 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES/IMIDAZOLE PH 6.5, 30 REMARK 280 MM MGCL2, 30 MM CACL2, 10% PEG 4000, 20% GLYCEROL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.74500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.33500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.00500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.33500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.74500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.00500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 CYS A 347 REMARK 465 GLU A 348 REMARK 465 GLU A 349 REMARK 465 THR A 350 REMARK 465 SER A 351 REMARK 465 LEU A 352 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 176 CD CE NZ REMARK 470 ASP A 178 CG OD1 OD2 REMARK 470 LYS A 180 CG CD CE NZ REMARK 470 GLU A 182 OE1 OE2 REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 252 CG CD OE1 OE2 REMARK 470 LYS A 325 CG CD CE NZ REMARK 470 VAL A 346 CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2B ASP A 90 O HOH A 2021 2.17 REMARK 500 OD2B ASP A 90 O HOH A 2022 1.99 REMARK 500 NZ A LYS A 107 O HOH A 2030 1.84 REMARK 500 NE2B GLN A 137 O HOH A 2115 1.52 REMARK 500 OE2A GLU A 153 O HOH A 2153 1.81 REMARK 500 OE1B GLU A 153 O HOH A 2153 2.15 REMARK 500 OE2 GLU A 204 O HOH A 2219 2.15 REMARK 500 OE1A GLU A 230 O HOH A 2105 2.08 REMARK 500 OE1B GLU A 230 O HOH A 2105 2.11 REMARK 500 OE1 GLU A 287 O HOH A 2260 1.74 REMARK 500 OE1A GLN A 288 OH TYR A 319 2.17 REMARK 500 NH1B ARG A 299 O HOH A 2286 1.85 REMARK 500 CG B HIS A 339 O HOH A 2079 2.10 REMARK 500 ND1B HIS A 339 O HOH A 2079 2.07 REMARK 500 CD2B HIS A 339 O HOH A 2079 1.40 REMARK 500 CE1B HIS A 339 O HOH A 2079 1.42 REMARK 500 NE2B HIS A 339 O HOH A 2079 0.66 REMARK 500 O HOH A 2041 O HOH A 2330 2.16 REMARK 500 O HOH A 2055 O HOH A 2061 2.08 REMARK 500 O HOH A 2077 O HOH A 2196 2.04 REMARK 500 O HOH A 2095 O HOH A 2096 1.98 REMARK 500 O HOH A 2111 O HOH A 2183 2.07 REMARK 500 O HOH A 2114 O HOH A 2115 2.10 REMARK 500 O HOH A 2157 O HOH A 2186 1.86 REMARK 500 O HOH A 2175 O HOH A 2234 1.64 REMARK 500 O HOH A 2185 O HOH A 2186 1.95 REMARK 500 O HOH A 2210 O HOH A 2215 2.19 REMARK 500 O HOH A 2242 O HOH A 2287 2.00 REMARK 500 O HOH A 2285 O HOH A 2316 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2013 O HOH A 2310 4565 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 209 CD GLU A 209 OE1 0.074 REMARK 500 GLU A 209 CD GLU A 209 OE2 0.514 REMARK 500 GLU A 209 CG GLU A 209 CD 0.153 REMARK 500 CYS A 215 CB CYS A 215 SG -0.101 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 209 CG - CD - OE2 ANGL. DEV. = -21.5 DEGREES REMARK 500 GLU A 209 OE1 - CD - OE2 ANGL. DEV. = 9.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 219 64.88 -105.32 REMARK 500 SER A 266 37.51 -145.66 REMARK 500 HIS A 276 -65.42 -128.25 REMARK 500 ASN A 311 34.19 -86.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1351 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 163 O REMARK 620 2 GLN A 212 OE1 122.4 REMARK 620 3 HOH A2012 O 83.3 92.7 REMARK 620 4 HOH A2333 O 77.9 159.0 95.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1347 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1348 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1349 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1352 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZNX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OTU DOMAIN OF OTULIN D336A REMARK 900 MUTANT DBREF 3ZNV A 80 352 UNP Q96BN8 F105B_HUMAN 80 352 SEQADV 3ZNV GLY A 78 UNP Q96BN8 EXPRESSION TAG SEQADV 3ZNV PRO A 79 UNP Q96BN8 EXPRESSION TAG SEQRES 1 A 275 GLY PRO LEU SER VAL ALA PRO GLU MET ASP ILE MET ASP SEQRES 2 A 275 TYR CYS LYS LYS GLU TRP ARG GLY ASN THR GLN LYS ALA SEQRES 3 A 275 THR CYS MET LYS MET GLY TYR GLU GLU VAL SER GLN LYS SEQRES 4 A 275 PHE THR SER ILE ARG ARG VAL ARG GLY ASP ASN TYR CYS SEQRES 5 A 275 ALA LEU ARG ALA THR LEU PHE GLN ALA MET SER GLN ALA SEQRES 6 A 275 VAL GLY LEU PRO PRO TRP LEU GLN ASP PRO GLU LEU MET SEQRES 7 A 275 LEU LEU PRO GLU LYS LEU ILE SER LYS TYR ASN TRP ILE SEQRES 8 A 275 LYS GLN TRP LYS LEU GLY LEU LYS PHE ASP GLY LYS ASN SEQRES 9 A 275 GLU ASP LEU VAL ASP LYS ILE LYS GLU SER LEU THR LEU SEQRES 10 A 275 LEU ARG LYS LYS TRP ALA GLY LEU ALA GLU MET ARG THR SEQRES 11 A 275 ALA GLU ALA ARG GLN ILE ALA CYS ASP GLU LEU PHE THR SEQRES 12 A 275 ASN GLU ALA GLU GLU TYR SER LEU TYR GLU ALA VAL LYS SEQRES 13 A 275 PHE LEU MET LEU ASN ARG ALA ILE GLU LEU TYR ASN ASP SEQRES 14 A 275 LYS GLU LYS GLY LYS GLU VAL PRO PHE PHE SER VAL LEU SEQRES 15 A 275 LEU PHE ALA ARG ASP THR SER ASN ASP PRO GLY GLN LEU SEQRES 16 A 275 LEU ARG ASN HIS LEU ASN GLN VAL GLY HIS THR GLY GLY SEQRES 17 A 275 LEU GLU GLN VAL GLU MET PHE LEU LEU ALA TYR ALA VAL SEQRES 18 A 275 ARG HIS THR ILE GLN VAL TYR ARG LEU SER LYS TYR ASN SEQRES 19 A 275 THR GLU GLU PHE ILE THR VAL TYR PRO THR ASP PRO PRO SEQRES 20 A 275 LYS ASP TRP PRO VAL VAL THR LEU ILE ALA GLU ASP ASP SEQRES 21 A 275 ARG HIS TYR ASN ILE PRO VAL ARG VAL CYS GLU GLU THR SEQRES 22 A 275 SER LEU HET GOL A1347 6 HET GOL A1348 6 HET GOL A1349 6 HET GOL A1350 6 HET CA A1351 1 HET CL A1352 1 HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 3 CA CA 2+ FORMUL 4 CL CL 1- FORMUL 5 HOH *333(H2 O) HELIX 1 1 ILE A 88 TRP A 96 1 9 HELIX 2 2 THR A 100 GLN A 115 1 16 HELIX 3 3 TYR A 128 GLN A 141 1 14 HELIX 4 4 PRO A 146 ASP A 151 1 6 HELIX 5 5 PRO A 152 TYR A 165 1 14 HELIX 6 6 ASN A 166 TRP A 171 5 6 HELIX 7 7 ASP A 183 MET A 205 1 23 HELIX 8 8 THR A 207 PHE A 219 1 13 HELIX 9 9 GLU A 222 LYS A 249 1 28 HELIX 10 10 PRO A 254 ARG A 263 1 10 HELIX 11 11 ASP A 268 HIS A 276 1 9 HELIX 12 12 LEU A 277 VAL A 280 5 4 HELIX 13 13 GLU A 287 ARG A 299 1 13 HELIX 14 14 SER A 308 TYR A 310 5 3 HELIX 15 15 THR A 312 GLU A 314 5 3 SHEET 1 AA 6 MET A 86 ASP A 87 0 SHEET 2 AA 6 SER A 119 ARG A 121 -1 O ILE A 120 N MET A 86 SHEET 3 AA 6 HIS A 339 VAL A 344 -1 O ILE A 342 N ARG A 121 SHEET 4 AA 6 VAL A 329 ASP A 336 -1 O ILE A 333 N ASN A 341 SHEET 5 AA 6 THR A 301 ARG A 306 1 O THR A 301 N VAL A 330 SHEET 6 AA 6 ILE A 316 TYR A 319 -1 O THR A 317 N VAL A 304 LINK CA CA A1351 O SER A 163 1555 2674 2.45 LINK CA CA A1351 OE1BGLN A 212 1555 1555 2.42 LINK CA CA A1351 O HOH A2012 1555 1555 2.36 LINK CA CA A1351 O HOH A2333 1555 1555 2.30 CISPEP 1 TYR A 319 PRO A 320 0 -13.95 SITE 1 AC1 6 HIS A 276 GLN A 279 GLY A 284 GLY A 285 SITE 2 AC1 6 GLU A 287 GLU A 290 SITE 1 AC2 7 TRP A 167 ASP A 268 PRO A 269 GLY A 270 SITE 2 AC2 7 GLN A 271 ARG A 274 GOL A1350 SITE 1 AC3 8 GLU A 95 TRP A 96 ARG A 97 LYS A 116 SITE 2 AC3 8 GLN A 303 ARG A 345 HOH A2036 HOH A2291 SITE 1 AC4 7 TYR A 165 TRP A 167 ILE A 241 TYR A 244 SITE 2 AC4 7 ASN A 245 PRO A 269 GOL A1348 SITE 1 AC5 3 SER A 163 HOH A2012 HOH A2333 SITE 1 AC6 3 LYS A 94 VAL A 318 HOH A2315 CRYST1 43.490 72.010 94.670 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022994 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010563 0.00000